Human Gene LTN1 (ENST00000361371.10_12) from GENCODE V47lift37

JavaScript is disabled in your web browser

You must have JavaScript enabled in your web browser to use the Genome Browser

Description: listerin E3 ubiquitin protein ligase 1, transcript variant 1 (from RefSeq NM_015565.3)
Gencode Transcript: ENST00000361371.10_12
Gencode Gene: ENSG00000198862.14_15
Transcript (Including UTRs)
Position: hg19 chr21:30,300,466-30,365,198 Size: 64,733 Total Exon Count: 30 Strand: -
Coding Region
Position: hg19 chr21:30,302,770-30,365,126 Size: 62,357 Coding Exon Count: 30

Page Index	Sequence and Links	UniProtKB Comments	Primers	CTD	Gene Alleles
RNA-Seq Expression	Microarray Expression	RNA Structure	Protein Structure	Other Species	GO Annotations
mRNA Descriptions	Pathways	Other Names	Model Information	Methods

Data last updated at UCSC: 2024-08-22 23:36:26

Sequence and Links to Tools and Databases

Genomic Sequence (chr21:30,300,466-30,365,198)			mRNA (may differ from genome)		Protein (1766 aa)
Gene Sorter	Genome Browser	Other Species FASTA	Gene interactions	Table Schema	AlphaFold
BioGPS	Ensembl	Entrez Gene	ExonPrimer	GeneCards	HGNC
MGI	OMIM	PubMed	Reactome	UniProtKB	Wikipedia
BioGrid CRISPR DB

Comments and Description Text from UniProtKB


	ID: LTN1_HUMAN DESCRIPTION: RecName: Full=E3 ubiquitin-protein ligase listerin; EC=6.3.2.-; AltName: Full=RING finger protein 160; AltName: Full=Zinc finger protein 294; FUNCTION: E3 ubiquitin-protein ligase. E3 ubiquitin ligases accept ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfer the ubiquitin to targeted substrates (By similarity). PATHWAY: Protein modification; protein ubiquitination. INTERACTION: Q92985:IRF7; NbExp=2; IntAct=EBI-1044684, EBI-968267; P58753:TIRAP; NbExp=2; IntAct=EBI-1044684, EBI-528644; Q86WV6:TMEM173; NbExp=2; IntAct=EBI-1044684, EBI-2800345; PTM: Autoubiquitinated (By similarity). SIMILARITY: Belongs to the LTN1 family. SIMILARITY: Contains 1 RING-type zinc finger. SEQUENCE CAUTION: Sequence=AAF28910.1; Type=Frameshift; Positions=213, 328, 333, 342, 352, 354; Sequence=AAH29371.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence; Sequence=BAA34434.2; Type=Erroneous initiation; Note=Translation N-terminally shortened; Sequence=BAA91976.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=CAB90430.1; Type=Erroneous gene model prediction;

Primer design for this transcript

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3

Comparative Toxicogenomics Database (CTD)


	The following chemicals interact with this gene D000082 Acetaminophen D019256 Cadmium Chloride D013749 Tetrachlorodibenzodioxin C111118 2',3,3',4',5-pentachloro-4-hydroxybiphenyl C016403 2,4-dinitrotoluene D015123 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide D001564 Benzo(a)pyrene D005839 Gentamicins D010634 Phenobarbital D013759 Tetrahydrocannabinol more ... click here to view the complete list

Common Gene Haplotype Alleles


	Press "+" in the title bar above to open this section.

RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)


	Highest median expression: 7.85 RPKM in Testis Total median expression: 209.73 RPKM View in GTEx track of Genome Browser View at GTEx portal View GTEx Body Map

Microarray Expression Data


	Press "+" in the title bar above to open this section.

mRNA Secondary Structure of 3' and 5' UTRs

Region	Fold Energy	Bases	Energy/Base	Display As
5' UTR	-19.20	72	-0.267	Picture	PostScript	Text
3' UTR	-506.00	2304	-0.220	Picture	PostScript	Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

Protein Domain and Structure Information

InterPro Domains: Graphical view of domain structure
IPR011989 - ARM-like
IPR016024 - ARM-type_fold
IPR001841 - Znf_RING
IPR013083 - Znf_RING/FYVE/PHD

SCOP Domains:
48371 - ARM repeat
48431 - Lipovitellin-phosvitin complex, superhelical domain
57850 - RING/U-box
57903 - FYVE/PHD zinc finger

ModBase Predicted Comparative 3D Structure on O94822


Front	Top	Side

The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

Orthologous Genes in Other Species

Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.

Mouse	Rat	Zebrafish	D. melanogaster	C. elegans	S. cerevisiae
No ortholog	No ortholog	No ortholog	No ortholog	No ortholog	No ortholog
Gene Details	Gene Details
Gene Sorter	Gene Sorter
	RGD

Gene Ontology (GO) Annotations with Structured Vocabulary


	Molecular Function: GO:0004842 ubiquitin-protein transferase activity GO:0005515 protein binding GO:0008270 zinc ion binding GO:0016740 transferase activity GO:0046872 metal ion binding GO:0061630 ubiquitin protein ligase activity Biological Process: GO:0016567 protein ubiquitination GO:0051865 protein autoubiquitination

Descriptions from all associated GenBank mRNAs


	BC045726 - Homo sapiens cDNA clone IMAGE:4813307. AB018257 - Homo sapiens mRNA for KIAA0714 protein, partial cds. BC150284 - Homo sapiens ring finger protein 160, mRNA (cDNA clone MGC:166904 IMAGE:8860138), complete cds. JD201166 - Sequence 182190 from Patent EP1572962. JD502011 - Sequence 483035 from Patent EP1572962. JD420038 - Sequence 401062 from Patent EP1572962. JD071446 - Sequence 52470 from Patent EP1572962. JD279895 - Sequence 260919 from Patent EP1572962. BC140790 - Homo sapiens ring finger protein 160, mRNA (cDNA clone MGC:176467 IMAGE:9021658), complete cds. JD314667 - Sequence 295691 from Patent EP1572962. JD502268 - Sequence 483292 from Patent EP1572962. JD069044 - Sequence 50068 from Patent EP1572962. JD359320 - Sequence 340344 from Patent EP1572962. JD206028 - Sequence 187052 from Patent EP1572962. JD305712 - Sequence 286736 from Patent EP1572962. JD378389 - Sequence 359413 from Patent EP1572962. JD172457 - Sequence 153481 from Patent EP1572962. JD036431 - Sequence 17455 from Patent EP1572962. JD233159 - Sequence 214183 from Patent EP1572962. JD110827 - Sequence 91851 from Patent EP1572962. KJ904711 - Synthetic construct Homo sapiens clone ccsbBroadEn_14105 LTN1 gene, encodes complete protein. AB384515 - Synthetic construct DNA, clone: pF1KA0714, Homo sapiens ZNF294 gene for zinc finger protein 294, complete cds, without stop codon, in Flexi system. BC031633 - Homo sapiens cDNA clone IMAGE:5172245, containing frame-shift errors. AK001915 - Homo sapiens cDNA FLJ11053 fis, clone PLACE1004664. JD438782 - Sequence 419806 from Patent EP1572962. JD410793 - Sequence 391817 from Patent EP1572962. JD323512 - Sequence 304536 from Patent EP1572962. JD303052 - Sequence 284076 from Patent EP1572962. BC007525 - Homo sapiens zinc finger protein 294, mRNA (cDNA clone IMAGE:3533615), partial cds. AK023499 - Homo sapiens cDNA FLJ13437 fis, clone PLACE1002625. JD189963 - Sequence 170987 from Patent EP1572962. JD047281 - Sequence 28305 from Patent EP1572962. AF161350 - Homo sapiens HSPC087 mRNA, partial cds. BC029371 - Homo sapiens ring finger protein 160, mRNA (cDNA clone IMAGE:4048005), partial cds. AB621822 - Homo sapiens LTN1 mRNA for E3 ubiquitin-protein ligase listerin, partial cds, clone: HP08500-RBd56F02. JD225063 - Sequence 206087 from Patent EP1572962. JD276364 - Sequence 257388 from Patent EP1572962. JD477647 - Sequence 458671 from Patent EP1572962. JD342763 - Sequence 323787 from Patent EP1572962. JD224226 - Sequence 205250 from Patent EP1572962.

Biochemical and Signaling Pathways


	Reactome (by CSHL, EBI, and GO) Protein O94822 (Reactome details) participates in the following event(s): R-HSA-983157 Interaction of E3 with substrate and E2-Ub complex R-HSA-983147 Release of E3 from polyubiquitinated substrate R-HSA-983140 Transfer of Ub from E2 to substrate and release of E2 R-HSA-983168 Antigen processing: Ubiquitination & Proteasome degradation R-HSA-983169 Class I MHC mediated antigen processing & presentation R-HSA-1280218 Adaptive Immune System R-HSA-168256 Immune System

Other Names for This Gene


	Alternate Gene Symbols: A6NL41, A7E2D0, B2RTS0, C21orf10, C21orf98, C9J7U3, ENST00000361371.1, ENST00000361371.2, ENST00000361371.3, ENST00000361371.4, ENST00000361371.5, ENST00000361371.6, ENST00000361371.7, ENST00000361371.8, ENST00000361371.9, HSPC087, J3KPL4, KIAA0714, LTN1_HUMAN, NM_015565, O94822, Q05C47, Q9H8M4, Q9NUY5, Q9P0E9, RNF160, uc318can.1, uc318can.2, ZNF294 UCSC ID: ENST00000361371.10_12 RefSeq Accession: NM_015565.3 Protein: O94822 (aka LTN1_HUMAN)

Gene Model Information


	Click here for a detailed description of the fields of the table above.

Methods, Credits, and Use Restrictions


	Click here for details on how this gene model was made and data restrictions if any.